My brother and I were trying to take a photo of a passion flower in the garden, he with his Nikon D3 with 24-70mm f/2.8 and me with my Canon 5D MkII. Now I had perhaps argued incorrectly that I could get a sharper shot with my 85mm f/1.2 L II than he could with his zoom but his shots were better and I'm prepared to be corrected on the technical reasons as to why.

Lots of factors affect sharpness. The 85mm counts against you since you'll need a faster shutter speed to counter camera shake (at least 1/focal length). Also the minimum focusing distance of the 85mm lens is 0.95m which means the flower will occupy a smaller amount of the sensor compared to the 24mm lens which can focus much closer to the subject (the Canon version of this lens can be focused only 38cm from a subject). When you expand it to be the same size in both shots your image quality will suffer (though as you point out, the 5D Mark II is higher resolution than the D3 so this complicates matters). For a given aperture your image will have lower depth of field at 85mm compared to 24mm because of increased magnification.

I wanted to get the whole flower in focus therefore I figured I needed a DOF of 40mm, so by using the handy iPhone App 'Simple DOF' I dialled in 85mm lens, 1.5m focus distance and then increased the f/stop until it told me I had a DOF of about 40mm. Sounds straightforward to me but in practise the shots were disappointing.

You may know that the DOF is 40mm but you need to know exactly where to focus. DOF extends in front of, and behind, the focal point but it changes with focal length! Also the DOF calculation is only a guide. You've not given yourself any margin for error.

My brother then questioned why I was using my 85mm stopped down to f/2, when I could have just used another of my lenses at f/2.8 and perhaps got the same shot.

I would have the lens stopped down to at least f/8 for a shot like this (to ensure sufficient depth of field and good sharpness) and had the camera on a tripod for real image crispness. f/8 - 11 is the sweet aperture range for most lenses (above this the image deteriorates due to diffraction).

So, a quick visit to my local camera store and they suggested some interesting explanations to me:

1) "perhaps your 85mm lens is back-focusing, as most Canon lenses do, you should calibrate it using the micro-focus adjustment procedure." - One to investigate perhaps.

Microadjustment is worth doing with the 5D Mk II (since resolution is so high and the differences are visible) but is unlikely to be responsible in this situation.

2) "when using a shallow DOF at such a close focus distance the diameter of focus is very small, what you should have done was stop down to f/8 at least." - This one really surprised me, I have always thought about the settings required to get the DOF (i.e. 40mm in example above) but never thought that I needed to think about how the diameter of the focus area is affected.

I assume they're referring to the fact that the DOF will be shallow at wide apertures - see earlier.

3) "why did you use your 85mm lens when the minimum focusing point of your other lenses is shorter, therefore making it easier to get the shot?" - this one annoyed me after spending near £2k for a prime lens I thought I'd use it as I had expected it to be sharper.

I agree! The 85mm f/1.2 L lens is probably the best portrait lens in the world (and a favourite of mine, along with the 35mm f/1.4 L) and it's therefore designed for taking shots of head-sized objects! If I were doing the flower shot I'd have reached for my 100mm f/2.8 macro lens first of all, followed by my 24-70mm f/2.8 L (which can serve as a substitute for a macro lens since its minimum focusing distance is only 38cm).